[chimerax-users] Aligning volumes without resampling - Saving a map relative to another

[Elaine Meng]

Hi Helge,
As far as I know, you would have to resample in order to save one map relative to another and actually have the orientation saved in the file, as explained here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#afterfitting>

Theoretically you could just save the rotation/translation information instead, but then every time you open the map file, you have to apply that rotation/translation in an additional step.  See how to save/apply ChimeraX positions files:
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/positions.html>

See also "view matrix" and "measure rotation"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#rotation>

The other alternative is to save the session, which will retain the relative orientations.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jan 26, 2022, at 3:01 AM, Helge Paternoga via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi,
> 
> I would like to know if it is possible to save a .mrc map relative to another one. Basically, I would like to superpose two volumes and compare them outside of ChimeraX (i. e. using Coot) without resampling in ChimeraX, as it is my understanding that resampling changes the volume in question. I noticed that "fitmap" outputs the rotation etc. in the log, but I do not know if and how I can apply this to a map.
> 
> Many thanks in advance,
> 
> Helge